Better or Worse?
by beazlerat
Summary: After Danny's parents find out that he is phantom, thanks to the GIW, Danny is now on the run from both the GIW and his parents. With the only family that isn't trying to dissect him molecule by molecule out of reach, Danny has nowhere to go. SHIELD finds him and offers him a deal. Wonder if things will get better or worse?(Used to be called Family Ties)
1. Chapter 1

**Chapter One**

Danny's p.o.v

Danny walked along the streets of New York, his face covered by a hood and baseball cap. After his parents had found out he was Danny Phantom, thanks to the GIW, his parents now hated him. They teamed up with the GIW, and now the only people he could trust were still in Amity park. Jazz, Sam. and Tucker. Jazz refused to help anyone who would hurt Danny, and she had Sam and Tucker backing her up. The longer Danny dwelled on the memory of the three of the most important people to him, the more he felt like just collapsing and giving up the fight. So, he pushed those memories into the corner of his mind, and brought to light what was important at the moment.

First, he needed shelter and provisions. Second, he needed to figure out a way to keep the GIW off his tail, even though they (hopefully) had no idea where in the world he might be. He flew from Amity park,Minnesota to New York, the Big Apple, The City That Never Sleeps, and the rest of the names that people have started nicknaming it during the years. One reason he came to New York, was because of the Avengers. If he could stay in a huge city like this, it would be hard to find him. But the fact that it had superheroes was perfect, because that meant that he didn't have to Go Ghost. When he was in ghost form, he was a lot easier to track, compared to when he was in human form.

As Danny walked past a wall of TV's, he saw his face. Danny abruptly stopped, even though his logical side of his brain told him to hightail it outta there.

"Danny Fenton," says the news caster "has been kidnapped by the Public Enemy #1 of Amity Park, Danny Phantom, and it's rumored that Phantom has impersonated young Danny Fenton. A search has been issued across all of America. If you see anything concerning this young man, please call the number listed below. Now, for the rebuilding of the city of New York. Work has been…." That was enough for Danny. He walked briskly away, making sure his face was hidden. After wandering around until he got to an empty street, he leaned against a wall and took a shaky breath. It was enough that most of Amity used to hate him, now he had all of America after him, and probably the police and government with his luck.

He pressed his back against the wall, and looked at the sky. Dusk was one of his favorite times, with all the colors blending together. He used to sit at his window, or go flying around at dusk, but now with all the buildings, he could barely see it at all. He sighed, and pushed off the wall, walking to who knows where, hoping with all his might that this wasn't actually happening. But, sadly, it was.

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 **Hey guys! I'm new to writing fanfiction, so I welcome criticism, but no flamers please! I really hope you enjoyed this story, please review. I don't own DP or Avengers.**

 **-Beazle**


	2. Chapter 2

**Chapter two**

Danny p.o.v

Danny glanced down at my watch, with the numbers 9:00 AM staring back at him. It had been less than 24 hours since his parents had found out, since he ran away, since the GIW finding out about him being a halfa, and since his life became a living nightmare.

he had been walking all night, trying to keep moving so that it would be easier to hide. Danny couldn't relax, all he could do was try his best to not break down. Him being able to transform into a human was what threw the GIW off the most. They couldn't find him because a human can't be half dead, or at least they think. Scratch that, or at least they thought. Now that his cover was blown, there was nowhere to hide.

Danny sighed, and then stiffened up. He glanced around, and then locked eyes with someone that was staring right at him. The man grinned at Danny, and that grin sent shiver down Danny's spine. He lifted his phone to his ear and spoke into it. Danny quickened his pace, and turned down an empty alley. As soon as the man was out of sight, he began sprinting as fast as he could, taking random turns down alley ways. As he turned a corner, something shot into his shoulder. He fell back with a gasp of pain.

"Well, if it isn't the ghost freak. Ready for some painful experiments?" Whoever was talking, Danny couldn't see. The pain in his shoulder was making his vision blur, and he could feel himself slowly blacking out. Someone grabbed the front of his shirt, and pulled him up roughly, but then dropped him. The pain in his shoulder exploded, and he momentarily forgot to breathe. The last thing he saw was a figure standing over him, reaching his arm out to him.

As Danny woke up, he expected to see his room, with his NASA posters, and his rocket and planet models, and his desk sitting in the corner with a stack of unfinished homework assignments that Mr. Lancer had given out. But here, that was not the case. He was in a bed, with an IV tube in his arm, along with bandages wrapped around his left shoulder, and (thankfully) no hospital gown. He jerked into a sitting position and reached to take out the IV tube.

"Well look who is up?" Danny jerked his head towards the voice and saw a man with brown hair and glasses wearing a white coat over his clothes. "Who are you? Where am I?" Danny shot out before he could stop himself. The man blinked in surprise. "I'm Doctor Rigor, and this is the SHIELD headquarters." The boy stayed tense, and then tried to sit up but Dr. Rigor pushed him back down. "You have a very bad burn on your right shoulder that needs to get healed and we need to ask you a few questions, Mr. Fenton." At the sound of his last name, Danny sharply inhaled. With that, Dr. Rigor stood up and went out the door, most likely to go and get who ever was to question him. As soon as the door closed, Danny nimbly jumped out of bed, swiftly pulled the IV tube, and pulled the closet door open, and luck be with him, there was a shirt and jacket folded up. With that, he entered the closet and tried to make his escape.

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 **I am SOOOOO sorry that I didn't update when I said I would. Writers block will be the death of me and probably all writers. I really hoped you liked this chapter, and I am sorry that it isn't that long, but I still have some writers block. Please review, and tell me what you think!**

 **-Beazle**


	3. Chapter 3

He tried to go ghost.

And it worked! He flew out, and kept living his life, with no super secret government on his tail!

But, if that happened, I wouldn't have a story to tell. So, here is what really happened. It didn't work, and Danny felt panic begin to crawl up his throat. He took a deep breath and tried to remember what could have caused him to lose his powers. He went back to when the GIW shot him, and then it struck him. They had hit him with the plasmius maximus. He wouldn't be able to use his powers for maybe another few hours. He suppressed a groan, and nearly banged his head on the closet wall.

With a small sigh, he began to look around and find something, anything, that could be useful in helping him _get out of here._ After a brief glance around, he found nothing useful. That is, until he happened to glance up and found an air vent cover. He grinned and began unscrewing the cover. He had no idea why they were so easy to unscrew, but that didn't seem important right now. He had to get out of here, because even if they wanted to help him, if he stayed here too long the GIW would be able to pick up his ecto-signature. And, who on Earth calls themselves SHEILD? It probably stands for some long, and forgettable name, but _still._

After heaving himself up into the vent, careful not to hurt his shoulder, he began to army crawl. There wasn't really any forks to choose between, it was all just one long, very small and uncomfortable tunnel that turned occasionally.

After doing this for about 10 minutes, he hit a dead end. The only thing was another vent cover, with voices coming from it. Danny crawled toward it to listen to the conversation. Curiosity killed the cat, but he was already half dead, so might as well listen into a conversation that was probably just wasting his time.

"O.k Fury, can finally tell us who that kid was and why you sent a team of agents to come pick him up?" Danny couldn't see who it was that was talking, he could barely see through the vent cover, much less make out faces. The vent was in the wall, about head height, and he could barely make out that there was a group of people around a table.

"Daniel James Fenton, born in Amity Park, Illinois, to Jack and Maddie Fenton, the leading experts in ghosts. Yesterday we gathered footage of Daniel getting attacked by the Guys in White, also known as the GIW. They were cut from government funding a month ago due to the fact that they couldn't get anything done. They have been off the grid since yesterday, and only came up when Rogers stopped them from getting to Daniel." A second voice started talking, and this voice was obviously the leader, and had obviously done his research. "O.k. you know a lot about this kid, but why are the GIW after a kid that can't even be 17?"

There was a pause and some background noise, and then the second voice said, "Danny Phantom," Danny's breath caught in his throat and he tried not to make any sound," is Amity Parks superhero. There is multiple footage of him fighting ghosts-" "Ghosts!" The second voice was cut off by a third,"Fury, Ghosts don't exist. I can believe in aliens, and Norse gods, but ghosts?" The voice that Danny now knew as Fury, kept on talking,"No ones knows where he came from, but he appeared around the same time as the Fenton's completed their ghost portal. He has saved the town multiple times from different ghosts that have threatened the townsfolk safety. The GIW and the Fenton's have been trying to capture and contain him, with failed efforts. New evidence has proven that Daniel is Phantom, how, we are not sure, but I am sure that he would like to explain seeing as he is listening in on this conversation in the vents." After that last part, nobody made a sound, until the vent cover was taken off and Danny found himself looking into _Steve-Freaking-Rogers,_ a.k.a, Danny's life long hero.

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 **IMPORTANT**

 **Hello! I am so sorry that I haven't updated in a while, and I am so sorry that I am not good at making long chapters, but I hope you enjoy this. I changed a few things in the first 2 chapters. I was told that Amity was in Illinois, and even though the internet says that it is in Minnesota, I completely agree that it should be in Illinois. Also, i changed that instead of Doc. Banner being there when Danny wakes up, it is a random SHIELD doctor, and instead of the Avengers tower, it is SHIELD HQ. Also, in the second chapter it says mistake, but I meant to type escape. i am very sorry if that confused you. ALSO! I want to change the title of my story, any suggestions? Thank you all! constructive criticism is welcome.**

 **-Beazle**


	4. Chapter 4

"Uhh…" Danny was too starstruck to give an answer that actually sounded intelligent. But, who can blame him? He finally meets the person that inspired him to become a hero, what do you think Danny will do, strike up a friendly conversation? "Are you actually a ghost?" someone behind Steve asked. Steve turned his head to look at whoever was talking, and that let Danny see who else was in the room. There was Blackwidow, Sam's favorite Avenger, Ironman, Tucker's favorite, Hawkeye, Jazzs favorite, Captain America, Danny's favorite superhero, and Bruce Banner, Danny's favorite scientist. He had stumbled on some of Dr. Banners work, and had been hooked. Plus, he could relate to the guy. It is a pain to have the government after you all the time. In the very back of the room, was an African-American man with an eye-patch, who he guessed was Fury.

"Are you actually a ghost?" Apparently Ironman was the person that had asked the question. Steve Rogers ( Danny was internally screaming) ignored Tony Stark ( more internal screaming) and turned back to Danny. "Do you want some help getting out of the vent?" Danny, still too starstruck to speak, nodded. Steve reached out and grabbed Danny's arms, and slid him out of the vent catching him before he could face plant. The movement had jarred his shoulder, and Danny had to bite his tongue to keep from making any noise. Luckily the pain was like a splash of water to the face and Danny was able to think straight.

After a second of silence, Man-Who-Might-Be-Fury started walking out of the room, throwing a "With me Mr. Fenton," over his shoulder. After a brief hesitation, Danny followed. The hallway was short and neither of them said a word. What do you say to a man who knows everything about you? After what seemed like an eternity, they entered a room that with a desk and a chair. As soon as the door was shut, Fury turned around and the sound of a lock being engaged seemed to cut through the air like a bullet. Danny's head whipped around to look behind him, and tried the door handle.

It didn't budge.

Danny slowly turned around to face the one-eyed man, staying close to the door. "Why is the door locked?" Danny asked quietly, hoping that at least he could break the ice. "We need this chat to be private, and I also need you to stay here. You have been seen doing dangerous and illegal activities, so I am taking precaution. We know that whatever you were shot with has temporarily rendered your powers unavailable, and we would like to know how long." Danny shifted slightly, and then asked a question of his own, "Are you with the GIW?" Fury stayed stone faced as he answered. "We are with the government-" Danny backed up till his back hit the door, face pale "but we are not with the GIW. They were disbanded a month ago, and are running on what we believe is stolen money." Danny visibly relaxed, but stayed standing near the door. "When can I leave?" "We'd like you to answer some of our questions, then we can decide." Danny paused, then nodded, "Why did you steal those jewels and kidnap the mayor?" He groaned before Fury even finished his sentence, running a hand through his pitch black hair "I have tried to tell people my side of those stories for ages. For the mayor, he was being overshadowed -possessed I guess I should say- by an evil ghost sheriff who wanted to punish me for no reason, and for the stolen jewels, long story short I was being mind controlled into doing that stuff by an evil circus master who had a magic staff that my friends were able to break." After his rant, he glanced up and rubbed the back of his neck sheepishly "Sorry," he muttered.

"Overshadowed?" Asked Fury, still having no emotion show on his face. "Yeah, ghosts can do that to people by going intangible. They rarely ever do it, and I especially hate doing it. It feels… I don't know, wrong, to take away someone's free will." Danny refused to meet Fury's gaze because he was intimidating. Danny had faced the King of Ghosts, and he was intimidated by a pirate. He wasn't even a _ghost_ pirate. After a long minute of silence (wow, this man did not talk much), Danny looked up at him from under his bangs. "Why do you protect Amity?" The ebony haired teen sighed and leaned against the wall next to the door. "Every single scientist that studies ectology, thinks that all ghosts are evil. They're not. Some are good, some are bad, and some just want to live normally. Only the bad ghosts come out of the Ghost Portal. My parents," Danny stopped for a second to swallow the lump in his throat, "and the Guys in White are actually really bad at ghost hunting, so me, Sam, Tucker, and sometimes Jazz do it for them. Plus, we actually treat ghost humanly."

"How did you become Danny Phantom?" After hesitating for a second, Danny answered. "Lab accident. When the portal didn't work, and when it was just me, Sam, and Tucker, I went in and accidentally hit the on switch. The portal activated… with me inside. I got hit with ectoplasm and 10,000 volts of energy, fusing the ectoplasm with my molecules." Danny grimaced at the memory. "Sounds painful," said Fury, even though there was no emotion to his voice or his face _still._ Danny was starting to wonder if the guy was even human, or if this was a robot talking to him. "You have no idea." He muttered. The sound of the lock disengaging startled Danny, prompting him to look the only other occupant in the room with wide eyes. "So… I can leave?" He asked hopefully. "No. You will instead be staying with the Avengers." Danny stood there with his mouth open, before he regained his senses. "Wait, what?"

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 **I am so sorry for not updating recently. I had no idea what to write, and then when I did have an idea I had to go Girls Camp, and for you writers out there you know that writing is torture and fun at the same time. I really hoped you enjoyed it, please tell if I can fix anything, and please don't kill me for taking so long to update. Hope you liked it! If I'm alive, I will try to update within a month at most. Thanks!**

 **-B. Rat**


	5. Chapter 5

**Sorry I haven't uploaded in a while, I took a nap.**

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"Join the Avengers? Are you kidding me? I just spent the last 24 hours of my life trying to figure out how to never stand out of the crowd, and now you want me to be an _Avenger?"_ Danny was honestly shocked with what pirate Fury had told him was going to happen. "No, ok? No. I am not doing this. I'm not working with the Avengers _and_ _with_ _the_ _government_."

"I know that the GIW has left a bad taste in your mouth when it comes to-"

Danny pushed off of the door he was leaning on and pulled it open.

"You don't have a choice." Danny paused and turned to Fury, "you can leave, but we both know that this is the best option, especially when at the moment you are powerless."

"It's only for a few more hours. Plus, I'm not sure I can-"

"Whether you work with the Avengers or don't, you are powerful. If a rogue agency like the GIW get to you, things will go downhill real fast. I don't care whether you help the Avengers or lounge around eating pringles all day, my only goal is to make sure that the wrong people don't get their hands on you."

There was a long pause, with neither of them speaking. Danny shifted a bit, "I'm glad that you seem to not want the GIW to strap me to a table, but what about your agency? SHIELD, or whatever, I'm sure some of your scientists are dying to get their hands on me." Fury didn't answer the question, turning away from Danny and walking to his desk. Instead only said "Make your choice Fenton." Well, that answered that. Now the question was whether to stay and see if the promise of protection was true, or leave and see if he could survive on his own. He stood for a minute still holding the door knob and the door still halfway open.

"No tests." No answer from Fury, who just turned and looked at Danny, "No tests and I'll agree to stay with the Avengers, and we'll see how it goes."

'/ -Line Break- c"|

Fury walked Danny back into the meeting room where the rest of the Avengers were. Fury was going to give them the basics of what would happen now that Danny had agreed, however the minute they stepped past the door frame Tony Stark spoke up.

"Why do you always say 'Going Ghost' when you change?"

"What?" When you meet one of the most famous and richest people in the world after they found out you are a scientific impossibility, you might be a bit shocked when out of all the things he could questions, was your catch-phrase.

"You always say going ghost when you change into your… other self."

"What else am I gonna say, 'guess I'll die'?" Danny's most prominent thought process was about how he hated himself for saying something that dumb to _the Tony Stark._

"Yeah, I'm still in denial that your a ghost." And how he didn't even believe in him!

It was at this point that Fury decided to interrupt and get the attention back to him. "Fenton will be staying with you for his protection from a rogue government agency called the GIW. Any questions?"

"Why?" This was _The_ Captain America asking this.

Fury turned to look at Danny. "We haven't been able to find out what, and ideas?"

"My best guess would be dissection," said Danny as he found sudden interest in his shoes, "To see how I and other ghosts tick, and to see if they can figure out how to power weapons with ectoplasm."

It was quiet after he had said that.

"I… thought that was an empty threat I heard when I found you being attacked. Just something to scare you." Danny glanced at the Captain, and shook his head.

"Well," Fury said as he turned to leave, "you'll be in good hands Fenton. Give me a call if you need anything, any of you." And left. Just like that, he was out the door.

"How old are you?" Danny turned, not at _all_ startled and no matter what they say _he did not jump in surprise,_ and saw that the very-terrifying-in-person Black Widow was addressing him.

"16." After that answer she just kind of, looked at him with a hard to read look.

"Woah, you are really young to be getting shot at." This time it was Hawkeye talking.

"Yeah, you know how life can be sometimes." Danny said with an awkward laugh, followed by him clearing his throat and shifting from one foot to another. Holy cow he must look like an idiot.

"Well, as lovely as this conversation has been," said Tony Stark while he slung his jacket over his shoulder, "I have a couple suit upgrades I've been working on and I'd like to get them started. So, Danny, if you wouldn't just follow me to the hangar."

"Hangar? What, it's too far to drive?" He turned and stared at Danny for a moment.

"You don't- You're telling me- Are you kidding me?! You don't know where you are, what the SHIELD HQ is?"

"...I guess? I woke up here, I wasn't awake for the ride. Are we on a ship?" Tony just grinned, and turned to keep walking down the hallway. He grabbed some sunglasses from his pocket and put them on.

"Come on team. I want to see the kid's face when he sees where we are."

Danny faltered a bit. If he was in space, as exciting as that would be, he was going to scream.

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 **Honestly though, I am sorry I haven't updated in a while. I started looking at all the people who had read this and the stress got to me. Would you guys start to hate my writing, will I just be super cliche about the story, will I have people love the story in the beginning and then hate it at the end, etc. Well, it's been on my mind this whole time, and I figured I should try again. I would also like to say the I really love constructive criticism (and compliments). I got one a while back telling me how to properly write dialogue, and at first I was kind of offended. However, while writing this chapter I found myself going back and looking at the comment when writing the dialogue. Really appreciated it Guest thank you! So, please don't get mad at me for taking a while. Better late than never am I right? Also, I don't know when I'll update, but I will try to do it monthly, and the chapters will be short. I'm sorry, but I feel like if I promise to much I'll get overwhelmed. Thanks, see you guys in a bit!**

 **-B. Rat**


	6. Chapter 6

**Hi! Look, I'm here! Like I said I would be! Enjoy! Sorry for all the exclamation points!**

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Danny wasn't on a ship, and he wasn't in space. The SHIELD HQ was a giant floating base in the sky. Normally he was fine with heights, enjoyed them even, but right now he was powerless and really couldn't do anything if he fell.

"Look at that Cap, priceless!" Tony Stark had been looking at Danny when they had exited the door leading to outside, and caught the whole process of Danny's double-take, and even when his jaw literally dropped. Danny closed his mouth before Stark could poke fun at him more, and cleared his throat.

"Tony." Steve Rogers said in a warning voice.

"The plane is this way." Black Widow lead Danny over to a plane on the deck. Well, the smaller plane on the deck of the way bigger plane that he was standing on. Yeah, he still hadn't wrapped his head around that fact yet.

"Do you have any stuff? Bags or anything?" Danny turned and saw that it was Dr. Banner talking. He had forgotten that he was there, to be honest. He hadn't said a word, well, at all when he was here.

"No, I was in too much a rush to get out of the house to really pack anything." Banner didn't respond, just kept walking to the plane.

~!~!~!~!~!~!~!~!~!~!~!~!~!~!~!~!~!~!~!~

The plane ride had been interesting, the view had definitely been nice. No one had really talked to him the whole time, Stark was reading the file that had Danny's whole life in it, and everyone else looked like they were still reeling from the fact that people wanted to dissect him.

They landed the plane, and drove to Stark tower.

"I'll take you to your room." Steve said as he was getting out of the car.

"Actually," Bruce Banner started as he got out of the car, "I think I will. I… I want to talk with Danny for a minute." The team seemed to respect that, and left, filing into the elevator. Banner waited for the doors to close before he turned to Danny and started talking.

"Was it a recreation of my experiment?" Was out before Danny could ask what he wanted to talk about.

"A- A recreation? No. My- well, my parents built a ghost portal." There was a pause.

"A ghost.. Portal? A portal to the realm of.. Ghosts?" Danny nodded.

"Why did you think it was a recreation of your experiment?" Banner stood for a minute, mulling things over.

"You come in with super powers and have the government coming after you for existing. That's about all the evidence I have, but it seemed pretty… familiar to my case. Ok now, let's talk about the… ghost portal that your parents built?"

"Yeah. They built it, it didn't work, they left, I went inside and accidentally turned it on. I got zapped with 10,000 volts that fused cytoplasm with my DNA. And now, I have ghost powers."

"Sounds painful."

"I get that a lot."

"I'm sure. Let's go up to your room." They walked to the elevator and Banner hit a button.

"I love your work by the way." Oh. My. Gosh. Danny had told himself that he wouldn't say it, he didn't want to mess up and embarrass himself.

"The fact that I turn into a giant green rage monster?"

"What? No, your other work. I've seen some of the articles you put online, and while I had to look up some words and theories, they were super cool."

"Thank you."

The rest of the ride they started talking about some more of Banners work. When they got to the floor, Banner stepped out of the elevator.

"Well, as much as I would love to keep talking, I'll let you get acquainted with your floor."

"Whoa, wait, did you say floor?!"

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 **Thank you so much everyone for all the support you gave! I really appreciated it. As always, criticism and compliments are welcome. If you have any ideas, feel free to share. I will be following the MCU story-line. I think. Gonna be honest here, I'm flying by the seat of my pants. Glad you like the story though! (I also edited the chapter right after I put it up. I don't know if you get updates for both, but that's the explanation. There was a mistake that would have bothered me for the rest of eternity if I didn't fix it.)**

 **-B. Rat**


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